A former top KGB agent on Monday won a tense run-off to lead Georgia's rebel pro-Russian region of South Ossetia after two earlier polls ended in turmoil and no recognition from the West.

The tiny republic's former security chief Leonid Tibilov was congratulated by his rival in Sunday's run-off and then promised to build a flourishing independent nation despite its lack of recognition from most of the world.

"We have won," the 60-year-old Tibilov told his supporters early Monday. "Now, we have to build a new and successful legitimate state," the local RES news agency quoted him as saying.

The commission said Tibilov won 54.12 percent of the vote with all ballots counted against human rights commissioner David Sanakoyev's 42.65 percent.

"We recognise the election and congratulate Leonid Tibilov on his victory," Sanakoyev was quoted as saying earlier Monday.

The peaceful end to the election contrasts sharply with the angry protests that followed a November 27 ballot in which a female candidate who opposed the local administration was disqualified after coming out ahead in the poll.

Alla Dzhioyeva was barred from the re-run election for alleged violations, and her supporters held 10 days of protests they dubbed the attempted "snow revolution".

She was then hospitalised in February after being interrogated and allegedly beaten by police following allegations that she planned to seize power.

Dzhioyeva did not register for the second ballot held March 25. The local authorities for their part have agreed not to press any more charges against her.

The drawn-out election process has caused some embarrassment in Moscow amid signs it was having trouble keeping reins on a territory whose independence it recognised after waging a controversial five-day war with Georgia in 2008.

Georgia has already dismissed the election as a sham.

"It's a continuation of farce and an imitation of elections in the Russian-occupied, ethnically cleansed region," Reintegration Minister Eka Tkeshelashvili told AFP.

Tibilov promised on Monday not to hound his political opponents and try to heal old wounds in a nation that is still struggling to recover from the war.

"I said in my election programme that I would not be dividing people into those who voted against me and those who supported me," he said. "I will work on uniting and rallying together the people of South Ossetia." Officials reported a 71.26-percent turnout and a total participation figure of 28,504 people -- a number watched closely due to Georgian claims of only 15,000 living in the region because of migration and wartime "ethnic cleansing".

The separatist authorities claim a total population figure of 70,000 and Monday's polling numbers are in line with their estimate.

Most South Ossetian residents hold Russian passports and 15,000 also voted in Russia's March 4 presidential polls. Official reports said 92.7 percent of them voted for president-elect Vladimir Putin.

The republic had been run with an iron fist since 2001 by Tskhinvali native Eduard Kokoity.

The one-time member of the championship winning Soviet wrestling team was a close Moscow ally who owed his career to Putin and at one stage declared South Ossetia's desire to join Russia.

The move was dismissed by Moscow as premature and Kokoity was more recently accused by local politicians of misappropriating Russia's financial aid.